Pathways Knowlegdes
Necessitatibus eius consequatur ex aliquid fuga eum quidem sint consectetur velit
| Pathway | DOIs | Note |
|---|---|---|
| nitrate reduction IX (dissimilatory) Accession ID: BioCyc:META_PWY0-1581 |
|
Garland PB, Downie JA, Haddock BA. Proton translocation and the respiratory nitrate reductase of Escherichia coli. Biochem J. 1975 Dec;152(3):547–59. PMID: 5996; PMCID: PMC1172508.; Miki K, Lin EC. Electron transport chain from glycerol 3-phosphate to nitrate in Escherichia coli. J Bacteriol. 1975 Dec;124(3):1288–94. doi: 10.1128/jb.124.3.1288-1294.1975. |
| succinate to cytochrome bo oxidase electron transfer Accession ID: BioCyc:META_PWY0-1329 |
- | |
| glycerol-3-phosphate to cytochrome bo oxidase electron transfer Accession ID: BioCyc:META_PWY0-1561 |
|
Schryvers A, Lohmeier E, Weiner JH. Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. Journal of Biological Chemistry. 1978 Feb;253(3):783–8. doi: 10.1016/s0021-9258(17)38171-1.; Freedberg WB, Lin ECC. Three Kinds of Controls Affecting the Expression of the glp Regulon in Escherichia coli. J Bacteriol. 1973 Sep;115(3):816–23. doi: 10.1128/jb.115.3.816-823.1973. |
| NADH to cytochrome bo oxidase electron transfer I Accession ID: BioCyc:META_PWY0-1335 |
- | |
| cyanate degradation Accession ID: BioCyc:META_CYANCAT-PWY |
|
Qian D, Jiang L, Lu L, Wei C, Li Y. Biochemical and Structural Properties of Cyanases from Arabidopsis thaliana and Oryza sativa. PLoS ONE. 2011 Mar 31;6(3):e18300. doi: 10.1371/journal.pone.0018300.; Rowlett RS, Tu C, McKay MM, Preiss JR, Loomis RJ, Hicks KA, Marchione RJ, Strong JA, Donovan GS, Chamberlin JE. Kinetic characterization of wild-type and proton transfer-impaired variants of beta-carbonic anhydrase from Arabidopsis thaliana. Arch Biochem Biophys. 2002 Aug 15;404(2):197–209. doi: 10.1016/s0003-9861(02)00243-6. PMID: 12147257.; Fett JP, Coleman JR. Characterization and expression of two cDNAs encoding carbonic anhydrase in Arabidopsis thaliana. Plant Physiol. 1994 Jun;105(2):707–13. PMID: 7520589; PMCID: PMC159412.; Murakami H, Sly WS. Purification and characterization of human salivary carbonic anhydrase. Journal of Biological Chemistry. 1987 Jan;262(3):1382–8. doi: 10.1016/s0021-9258(19)75797-4. |
| nitrite oxidation Accession ID: BioCyc:META_P282-PWY |
|
Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Archives of Microbiology. 1995 Jul 19;164(1):16–23. doi: 10.1007/s002030050230.; Yamanaka T, Fukumori Y. The nitrite oxidizing system of Nitrobacter winogradskyi. FEMS Microbiol Rev. 1988 Dec;4(4):259–70. doi: 10.1016/0378-1097(88)90246-7. PMID: 2856189.; Aleem MI, Hoch GE, Varner JE. Water as the source of oxidant and reductant in bacterial chemosynthesis. Proc Natl Acad Sci U S A. 1965 Sep;54(3):869–73. PMID: 5217465; PMCID: PMC219757. |
| L-alanine degradation II (to D-lactate) Accession ID: BioCyc:META_ALACAT2-PWY |
|
Schweiger G, Buckel W. On the dehydration of (R)-lactate in the fermentation of alanine to propionate by Clostridium propionicum. FEBS Letters. 1984 Jun 04;171(1):79–84. doi: 10.1016/0014-5793(84)80463-9. |
| 4-amino-3-hydroxybenzoate degradation Accession ID: BioCyc:META_PWY-7006 |
|
Marín M, Plumeier I, Pieper DH. Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway. J Bacteriol. 2012 Aug;194(15):3851–60. PMID: 22609919; PMCID: PMC3416551.; Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E. Uncovering the protocatechuate 2,3-cleavage pathway genes. J Bacteriol. 2009 Nov;191(21):6758–68. PMID: 19717587; PMCID: PMC2795304.; Takenaka S, Sato T, Koshiya J, Murakami S, Aoki K. Gene cloning and characterization of a deaminase from the 4-amino-3-hydroxybenzoate-assimilating Bordetella sp. strain 10d. FEMS Microbiol Lett. 2009 Sep;298(1):93–8. doi: 10.1111/j.1574-6968.2009.01699.x. PMID: 19594622.; ORII C, TAKENAKA S, MURAKAMI S, AOKI K. Metabolism of 4-Amino-3-hydroxybenzoic Acid byBordetellasp. Strain 10d: A Different ModifiedMeta-Cleavage Pathway for 2-Aminophenols. Bioscience, Biotechnology, and Biochemistry. 2006 Nov 23;70(11):2653–61. doi: 10.1271/bbb.60264. |
| 4-aminophenol degradation Accession ID: BioCyc:META_PWY-7081 |
|
Takenaka S, Okugawa S, Kadowaki M, Murakami S, Aoki K. The Metabolic Pathway of 4-Aminophenol in Burkholderia sp. Strain AK-5 Differs from That of Aniline and Aniline with C-4 Substituents. Appl Environ Microbiol. 2003 Sep;69(9):5410–3. doi: 10.1128/aem.69.9.5410-5413.2003. |
| nitrogen fixation I (ferredoxin) Accession ID: BioCyc:META_N2FIX-PWY |
|
Eady RR, Smith BE, Cook KA, Postgate JR. Nitrogenase of Klebsiella pneumoniae. Purification and properties of the component proteins. Biochem J. 1972 Jul;128(3):655–75. PMID: 4344006; PMCID: PMC1173817.; Vandecasteele J, Burris RH. Purification and Properties of the Constituents of the Nitrogenase Complex from Clostridium pasteurianum. J Bacteriol. 1970 Mar;101(3):794–801. doi: 10.1128/jb.101.3.794-801.1970. |
| ascorbate glutathione cycle Accession ID: BioCyc:META_PWY-2261 |
|
Macdonald IK, Badyal SK, Ghamsari L, Moody PCE, Raven EL. Interaction of Ascorbate Peroxidase with Substrates: A Mechanistic and Structural Analysis. Biochemistry. 2006 Jun 01;45(25):7808–17. doi: 10.1021/bi0606849.; Sharp KH, Moody PC, Brown KA, Raven EL. Crystal structure of the ascorbate peroxidase-salicylhydroxamic acid complex. Biochemistry. 2004 Jul 13;43(27):8644–51. doi: 10.1021/bi049343q. PMID: 15236572.; Chew O, Whelan J, Millar AH. Molecular Definition of the Ascorbate-Glutathione Cycle in Arabidopsis Mitochondria Reveals Dual Targeting of Antioxidant Defenses in Plants. Journal of Biological Chemistry. 2003 Nov;278(47):46869–77. doi: 10.1074/jbc.m307525200.; Shigeoka S, Ishikawa T, Tamoi M, Miyagawa Y, Takeda T, Yabuta Y, Yoshimura K. Regulation and function of ascorbate peroxidase isoenzymes. 2002 May 15;53(372):1305–19. doi: 10.1093/jxb/53.372.1305.; Noctor G, Foyer CH. ASCORBATE AND GLUTATHIONE: Keeping Active Oxygen Under Control. Annu Rev Plant Physiol Plant Mol Biol. 1998 Jun;49():249–79. doi: 10.1146/annurev.arplant.49.1.249. PMID: 15012235.; Jimenez A, Hernandez JA, Del Rio LA, Sevilla F. Evidence for the Presence of the Ascorbate-Glutathione Cycle in Mitochondria and Peroxisomes of Pea Leaves. Plant Physiol. 1997 May;114(1):275–84. PMID: 12223704; PMCID: PMC158303.; Patterson WR, Poulos TL. Crystal structure of recombinant pea cytosolic ascorbate peroxidase. Biochemistry. 1995 Apr 04;34(13):4331–41. doi: 10.1021/bi00013a023. PMID: 7703247.; Shigeoka S, Nakano Y, Kitaoka S. Purification and some properties of l-ascorbic acid-specific peroxidase in Euglena gracilis z. Archives of Biochemistry and Biophysics. 1980 Apr;201(1):121–7. doi: 10.1016/0003-9861(80)90495-6.; Shigeoka S, Nakano Y, Kitaoka S. Metabolism of hydrogen peroxide in Euglena gracilis Z by L-ascorbic acid peroxidase. Biochem J. 1980 Jan 15;186(1):377–80. PMID: 6768357; PMCID: PMC1161541. |
| superpathway of hydrolyzable tannin biosynthesis Accession ID: BioCyc:META_PWY-5478 |
|
Niemetz R, Gross GG. Enzymology of gallotannin and ellagitannin biosynthesis. Phytochemistry. 2005 Sep;66(17):2001–11. doi: 10.1016/j.phytochem.2005.01.009. PMID: 16153405.; Niemetz R, Gross GG. Ellagitannin biosynthesis: laccase-catalyzed dimerization of tellimagrandin II to cornusiin E in Tellima grandiflora. Phytochemistry. 2003 Dec;64(7):1197–201. doi: 10.1016/j.phytochem.2003.08.013. PMID: 14599517.; Beecher GR. Overview of Dietary Flavonoids: Nomenclature, Occurrence and Intake. The Journal of Nutrition. 2003 Oct;133(10):3248S–3254S. doi: 10.1093/jn/133.10.3248s.; Niemetz R, Gross GG. Oxidation of pentagalloylglucose to the ellagitannin, tellimagrandin II, by a phenol oxidase from Tellima grandiflora leaves. Phytochemistry. 2003 Feb;62(3):301–6. doi: 10.1016/s0031-9422(02)00557-5. PMID: 12620341.; Fröhlich B, Niemetz R, Gross GG. Gallotannin biosynthesis: two new galloyltransferases from Rhus typhina leaves preferentially acylating hexa- and heptagalloylglucoses. Planta. 2002 Nov;216(1):168–72. doi: 10.1007/s00425-002-0877-3. PMID: 12430027.; Niemetz R, Gross GG. Gallotannin biosynthesis: beta-glucogallin: hexagalloyl 3-O-galloyltransferase from Rhus typhina leaves. Phytochemistry. 2001 Nov;58(5):657–61. doi: 10.1016/s0031-9422(01)00300-4. PMID: 11672728.; Haslam E. Natural polyphenols (vegetable tannins) as drugs: possible modes of action. J Nat Prod. 1996 Feb;59(2):205–15. doi: 10.1021/np960040+. PMID: 8991956.; Haslam E, Cai Y. Plant polyphenols (vegetable tannins): gallic acid metabolism. Nat Prod Rep. 1994 Jan;11(1):41–66. doi: 10.1039/np9941100041. PMID: 15206456.; Hofmann AS, Gross GG. Biosynthesis of gallotannins: Formation of polygalloylglucoses by enzymatic acylation of 1,2,3,4,6-penta-O-galloylglucose. Archives of Biochemistry and Biophysics. 1990 Dec;283(2):530–2. doi: 10.1016/0003-9861(90)90678-r.; Cammann J, Denzel K, Schilling G, Gross GG. Biosynthesis of gallotannins: beta-glucogallin-dependent formation of 1,2,3,4,6-pentagalloylglucose by enzymatic galloylation of 1,2,3,6-tetragalloylglucose. Arch Biochem Biophys. 1989 Aug 15;273(1):58–63. doi: 10.1016/0003-9861(89)90161-6. PMID: 2757399. |
| formate to trimethylamine N-oxide electron transfer Accession ID: BioCyc:META_PWY0-1355 |
- | |
| nitrate reduction I (denitrification) Accession ID: BioCyc:META_DENITRIFICATION-PWY |
|
Knowles R. Denitrification. Microbiol Rev. 1982 Mar;46(1):43–70. doi: 10.1128/mr.46.1.43-70.1982.; Delwiche CC, Bryan BA. Denitrification. Annu Rev Microbiol. 1976;30():241–62. doi: 10.1146/annurev.mi.30.100176.001325. PMID: 10827. |
| formate to nitrite electron transfer Accession ID: BioCyc:ECO_PWY0-1585 |
|
Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev. 2002 Aug;26(3):285–309. doi: 10.1111/j.1574-6976.2002.tb00616.x. PMID: 12165429.; Tyson K, Metheringham R, Griffiths L, Cole J. Characterisation of Escherichia coli K-12 mutants defective in formate-dependent nitrite reduction: essential roles for hemN and the menFDBCE operon. Arch Microbiol. 1997 Nov;168(5):403–11. doi: 10.1007/s002030050515. PMID: 9325429.; Pope NR, Cole JA. Generation of a membrane potential by one of two independent pathways for nitrite reduction by Escherichia coli. J Gen Microbiol. 1982 Jan;128(1):219–22. doi: 10.1099/00221287-128-1-219. PMID: 6283015.; Abou-Jaoudé A, Chippaux M, Pascal MC. Formate-nitrite reduction in Escherchia coli K12. 1. Physiological study of the system. Eur J Biochem. 1979 Apr 02;95(2):309–14. doi: 10.1111/j.1432-1033.1979.tb12966.x. PMID: 37075. |
| cyanate degradation Accession ID: BioCyc:ECO_CYANCAT-PWY |
- | |
| superoxide radicals degradation Accession ID: BioCyc:MTBH37RV_DETOX1-PWY |
- | |
| hydrogen to trimethylamine N-oxide electron transfer Accession ID: BioCyc:META_PWY0-1578 |
|
Wissenbach U, Kröger A, Unden G. The specific functions of menaquinone and demethylmenaquinone in anaerobic respiration with fumarate, dimethylsulfoxide, trimethylamine N-oxide and nitrate by Escherichia coli. Arch Microbiol. 1990;154(1):60–6. doi: 10.1007/bf00249179. PMID: 2204318. |
| formate to nitrite electron transfer Accession ID: BioCyc:META_PWY0-1585 |
|
Simon J. Enzymology and bioenergetics of respiratory nitrite ammonification. FEMS Microbiol Rev. 2002 Aug;26(3):285–309. doi: 10.1111/j.1574-6976.2002.tb00616.x. PMID: 12165429.; Tyson K, Metheringham R, Griffiths L, Cole J. Characterisation of Escherichia coli K-12 mutants defective in formate-dependent nitrite reduction: essential roles for hemN and the menFDBCE operon. Arch Microbiol. 1997 Nov;168(5):403–11. doi: 10.1007/s002030050515. PMID: 9325429.; Pope NR, Cole JA. Generation of a membrane potential by one of two independent pathways for nitrite reduction by Escherichia coli. J Gen Microbiol. 1982 Jan;128(1):219–22. doi: 10.1099/00221287-128-1-219. PMID: 6283015.; Abou-Jaoudé A, Chippaux M, Pascal MC. Formate-nitrite reduction in Escherchia coli K12. 1. Physiological study of the system. Eur J Biochem. 1979 Apr 02;95(2):309–14. doi: 10.1111/j.1432-1033.1979.tb12966.x. PMID: 37075. |
| NADH to cytochrome bo oxidase electron transfer II Accession ID: BioCyc:META_PWY0-1567 |
|
Unden G, Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1997 Jul;1320(3):217–34. doi: 10.1016/s0005-2728(97)00034-0.; Tran QH, Bongaerts J, Vlad D, Unden G. Requirement for the Proton-Pumping NADH Dehydrogenase I of Escherichia Coli in Respiration of NADH to Fumarate and Its Bioenergetic Implications. European Journal of Biochemistry. 1997 Feb;244(1):155–60. doi: 10.1111/j.1432-1033.1997.00155.x.; Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM. Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain. J Bacteriol. 1993 May;175(10):3020–5. doi: 10.1128/jb.175.10.3020-3025.1993.; Ingledew WJ, Poole RK. The respiratory chains of Escherichia coli. Microbiol Rev. 1984 Sep;48(3):222–71. doi: 10.1128/mr.48.3.222-271.1984. |